Integrate mkbwt not building any index files

[Hannah Charlton]

Hi,

I am trying to use the Integrate tool to investigate fusions in a a couple of non-model organisms. I could get the test data to run without any problem, so I think the installation of Integrate itself is okay.

When I try and run Integrate mkbwt on my reference file devil.fa , it appears to run and load the reference file in fine:

../INTEGRATE$ ./Integrate mkbwt devil.fa
INTEGRATE version 0.2.6
Load ref
Chr1_supercontig_000000000  1   2180112
Chr1_supercontig_000000001  2180113 2553658
Chr1_supercontig_000000002  2553659 3628951
Chr1_supercontig_000000003  3628952 3803807

but then at the end it returns

ChrU_supercontig_000000438  3174687339  3174690241
ChrU_supercontig_000000439  3174690242  3174693010
8.94 seconds

build BWTs for whole genome
0.01 seconds

and finishes, seemingly with no errors but also with nothing in the ./bwts directory where I think it should be building the index.

I was wondering if there is maybe some particular formatting required for the reference .fa file? Or whether it doesn't work because this genome is made up of many contigs? Could I instead use something else to build .bwt and .rbwt indexes and put those into Integrate fusion? I'd appreciate any tips on how to get this working, as it looks like it could be a really useful tool for my project.

Thanks!
Hannah

[Jin]

There is an -mb option for both mkbwt and fusion. Try reduce the value to the length of the smallest contig you have.